Automatic validation and optimisation of biological models
Simulating the human heart is a challenging problem, with simulations being very time consuming, to the extent that some can take days to compute even on high performance computing resources. There is considerable interest in computational optimisation techniques, with a view to making whole-heart s...
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| Формат: | Дипломын ажил |
| Хэл сонгох: | English |
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2009
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| _version_ | 1826315940616208384 |
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| author | Cooper, J |
| author2 | McKeever, S |
| author_facet | McKeever, S Cooper, J |
| author_sort | Cooper, J |
| collection | OXFORD |
| description | Simulating the human heart is a challenging problem, with simulations being very time consuming, to the extent that some can take days to compute even on high performance computing resources. There is considerable interest in computational optimisation techniques, with a view to making whole-heart simulations tractable. Reliability of heart model simulations is also of great concern, particularly considering clinical applications. Simulation software should be easily testable and maintainable, which is often not the case with extensively hand-optimised software. It is thus crucial to automate and verify any optimisations. CellML is an XML language designed for describing biological cell models from a mathematical modeller’s perspective, and is being developed at the University of Auckland. It gives us an abstract format for such models, and from a computer science perspective looks like a domain specific programming language. We are investigating the gains available from exploiting this viewpoint. We describe various static checks for CellML models, notably checking the dimensional consistency of mathematics, and investigate the possibilities of provably correct optimisations. In particular, we demonstrate that partial evaluation is a promising technique for this purpose, and that it combines well with a lookup table technique, commonly used in cardiac modelling, which we have automated. We have developed a formal operational semantics for CellML, which enables us to mathematically prove the partial evaluation of CellML correct, in that optimisation of models will not change the results of simulations. The use of lookup tables involves an approximation, thus introduces some error; we have analysed this using a posteriori techniques and shown how it may be managed. While the techniques could be applied more widely to biological models in general, this work focuses on cardiac models as an application area. We present experimental results demonstrating the effectiveness of our optimisations on a representative sample of cardiac cell models, in a variety of settings. |
| first_indexed | 2024-03-06T19:53:22Z |
| format | Thesis |
| id | oxford-uuid:24b96d62-b47c-458d-9dff-79b27dbdc9f2 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-12-09T03:35:15Z |
| publishDate | 2009 |
| record_format | dspace |
| spelling | oxford-uuid:24b96d62-b47c-458d-9dff-79b27dbdc9f22024-12-01T18:49:22ZAutomatic validation and optimisation of biological modelsThesishttp://purl.org/coar/resource_type/c_db06uuid:24b96d62-b47c-458d-9dff-79b27dbdc9f2Software engineeringNumerical analysisApplications and algorithmsEnglishOxford University Research Archive - Valet2009Cooper, JMcKeever, SGavaghan, DWhiteley, JSimulating the human heart is a challenging problem, with simulations being very time consuming, to the extent that some can take days to compute even on high performance computing resources. There is considerable interest in computational optimisation techniques, with a view to making whole-heart simulations tractable. Reliability of heart model simulations is also of great concern, particularly considering clinical applications. Simulation software should be easily testable and maintainable, which is often not the case with extensively hand-optimised software. It is thus crucial to automate and verify any optimisations. CellML is an XML language designed for describing biological cell models from a mathematical modeller’s perspective, and is being developed at the University of Auckland. It gives us an abstract format for such models, and from a computer science perspective looks like a domain specific programming language. We are investigating the gains available from exploiting this viewpoint. We describe various static checks for CellML models, notably checking the dimensional consistency of mathematics, and investigate the possibilities of provably correct optimisations. In particular, we demonstrate that partial evaluation is a promising technique for this purpose, and that it combines well with a lookup table technique, commonly used in cardiac modelling, which we have automated. We have developed a formal operational semantics for CellML, which enables us to mathematically prove the partial evaluation of CellML correct, in that optimisation of models will not change the results of simulations. The use of lookup tables involves an approximation, thus introduces some error; we have analysed this using a posteriori techniques and shown how it may be managed. While the techniques could be applied more widely to biological models in general, this work focuses on cardiac models as an application area. We present experimental results demonstrating the effectiveness of our optimisations on a representative sample of cardiac cell models, in a variety of settings. |
| spellingShingle | Software engineering Numerical analysis Applications and algorithms Cooper, J Automatic validation and optimisation of biological models |
| title | Automatic validation and optimisation of biological models |
| title_full | Automatic validation and optimisation of biological models |
| title_fullStr | Automatic validation and optimisation of biological models |
| title_full_unstemmed | Automatic validation and optimisation of biological models |
| title_short | Automatic validation and optimisation of biological models |
| title_sort | automatic validation and optimisation of biological models |
| topic | Software engineering Numerical analysis Applications and algorithms |
| work_keys_str_mv | AT cooperj automaticvalidationandoptimisationofbiologicalmodels |